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Three-dimensional folding dynamics of the Xenopus tropicalis genome
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Three-dimensional folding dynamics of the Xenopus tropicalis genome
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Journal Article
Three-dimensional folding dynamics of the Xenopus tropicalis genome
2021
Overview
Animal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in
Xenopus tropicalis
embryos. First, TAD establishment in
X. tropicalis
is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that
X. tropicalis
is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.
Hi-C and single-molecule sequencing analysis provide an improved assembly of the
Xenopus tropicalis
genome and insights into three-dimensional genome dynamics throughout embryogenesis.
Publisher
Nature Publishing Group US,Nature Publishing Group
Subject
/ 631/136
/ 631/208
/ 631/337
/ 631/80
/ Animal Genetics and Genomics
/ Animals
/ Apoptosis Regulatory Proteins - genetics
/ Biomedical and Life Sciences
/ Cell Cycle Proteins - genetics
/ Chromatin Assembly and Disassembly
/ Computational Biology - methods
/ DNA
/ Embryonic Development - genetics
/ Embryos
/ Gene Expression Regulation, Developmental
/ Genome
/ Genomes
/ Principal components analysis
/ Proteins
/ Xenopus
